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ecoPCR

* DNA barcoding is a tool for characterizing the species origin using a short sequence

from a standard position and agreed upon position in the genome. To be used as a DNA barcode,
a genome locus should vary among individuals of the same species only to a minor degree and it
should vary among species very quickly. From a practical point of view, a barcode locus should be
ﬂanked by two conserved regions to design PCR primers. Several manually discovered
barcode loci like COI, rbcL, 18S, 16S and 23S rDNA, or trnH-ps are routinely used today, but no
objective function has been described to measure their
quality in terms of universality (barcode coverage, Bc ) or in terms of taxonomical discrimination
capacity (barcode speciﬁcity, Bs ).

ecoPCR is an electronic PCR software developed by LECA (LECA) and Helix-Project (HELIX). It helps you to estimate Barcode primers quality. In conjunction with OBITools you can postprocess ecoPCR output to compute barcode coverage and barcode speciﬁcity.
New barcode primers can be developed using the ecoPrimers software

Currently, ecoPCR is available as a local program that you can download and install on unix like machine.